You can split those clones by folder now. In the Agents sidebar, open the grouping control and set Grouping to Workspace. That gives each local folder its own section. Cursor-managed worktrees under ~/.cursor/worktrees still stay grouped with the source repo.
Same notes here: Worktree chats no longer get their own sidebar tab — all chats grouped under main repo (Glass / recent update)
This thread is closed, so if it still merges after you update to the latest, please start a new thread.